The peripheries of rare-metal metallogenic systems frequently host skarn-type or hydrothermal vein-type Pb-Zn deposits, though their genetic connections with parental systems remain debated. The newly identified Gariatong W-Mo polymetallic metallogenic system in the Lhasa Terrane displays well-defined Nb-Ta-Rb, Mo-W, W-Mo, W-Bi, and Pb-Zn-Ag metallogenic zoning, establishing it as an exemplary site for investigating genetic relationships between Pb-Zn and rare-metal mineralization. This investigation targets skarn-type Pb-Zn deposits spatially associated with rare-metal orebodies at Gariatong, utilizing integrated analytical approaches, including in situ LA-ICP-MS trace-element analysis of sulfides, sulfur isotope geochemistry, and LA-ICP-MS elemental mapping of sphalerite, to constrain metal sources, characterize fluid evolution, and establish genetic correlations with the rare-metal system. Key findings include the following: (1) sphalerite shows enrichment in Fe, Mn, Co, and Cd, while pyrite contains elevated As, Pb, Co, Cu, and Mn. Fe, Cd, and Mn primarily occur as solid solutions or nanoparticles, whereas As and Pb exist as micro-inclusions. (2) Sphalerite Zn/Cd ratios (73.6–184) and Co-Ni-As ternary diagrams confirm a magmatic–hydrothermal skarn origin. (3) Mineralization occurred under moderate-temperature, mildly oxidized conditions, as constrained by sphalerite Fe contents and mineral assemblages. Sulfur isotope compositions (δ³⁴S = −1.0‰ to 3.2‰; mean: 1.9‰) indicate a magmatic sulfur source. This study reveals that the Nb-Ta-Rb mineralization, quartz-vein- and greisen-type W-Mo deposits, and skarn-type Pb-Zn orebodies—all genetically associated with highly fractionated granites—constitute an integrated magmatic–hydrothermal system with vertical (depth-related) zoning relative to the granitic intrusion. These results provide critical constraints for understanding rare-metal–Pb-Zn genetic associations and suggest that Pb-Zn mineralization may serve as a key exploration indicator for rare metals in the Lhasa Terrane.